Comparative Chloroplast Genomics Of Aceraceae Species

The family Aceraceae is the important tree species with the ecologically and economically important values,widespread in the Northern hemisphere.Abundant fossil records of the Aceraceae have been recorded.Recently,the phylogenetic anlaysis showed support to the placement of Acer and Dipteronia in the traditional family Aceraceae as sole members-in Sapindaceae.Our initial attempts confirmed that large amounts of phylogenetically useful data could be generated rapidly,and a result of increased phylogenetic resolution and species divergence for Aceraceae species.The main theme of our study is as follows:Sequences of chloroplast genomes(cp DNA)of 19 Acer species are used with 17 published data to determine the variations in the sequences,phylogeny and evolutionary divergence of Aceraceae species.The chloroplast genome of Acer species ranged in size from 159,705 bp(A.ginnala)to 156,946 bp(A.cinnamomifolium).The genome structure,gene order,and GC content of Acer species were almost similar to those of other higher plant plastid genomes.Most prominently we observed that A.fenzellatum has the lowest GC contents in LSC and SSC regions as compared to the IR region and the cp genome size of A.cinnamomifolium was smaller than that of LSC and SSC.The overall AT content of Acer chloroplast genomes was 62.2%,while the corresponding values of the LSC,SSC,and IR regions were 64.0%,67.8%,and 57.3%,respectively.In previous studies mostly angiosperms contained 74 protein-coding genes some of the cpDNA of Aceraceae contained 134 genes,including 86 protein-coding genes(78 PCG species),eight ribosomal RNA genes(4 rRNA species)and 40 tRNA genes(31 tRNA species).Generally,we analyzed three kinds of repeats(dispersed,tandem and palindromic)studied in the Acer species.Also,we examined that the A.ginnala has the largest repeat numbers,i.e.,tandem and tRNA or gene similar like 48 and 40 whereas dispersal and palindromic were 23 and 16 repeats,respectively.Dispersed and palindromic were almost equal in all Acer species,A.flabellatum has the highest palindromic number whereas A.cinnamomifolium has the lowest dispersed number and A.mono Maxim shows great differences when compared with other species.Overall,we found that tandem and tRNA or gene similar had the largest number of repeats as 36% and 32% whereas dispersed and palindromic harbored fewer repeats as 18% and 14%.Moreover,we identified 11 hotspot regions trnH(GUG),trnR(UCU)-atpA,psbZtrn G(UCC),trnG(UCC),trnfM(CAU)-trnfM(CAU),rps16,rps14,rps19,rpl22,rpl32,and ycf1 which could be useful molecular genetic markers for future phylogenetic studies.Interestingly,we determined 14 chloroplast genes as a result of site-specific selection analysis with coding sites(atpA,atpB,ndhA,ndhD,ndhF,rbcL,rpoA,rpoB,rpoC1,rpoC2,rps8,rps19,ycf1 and ycf2)were under protein sequence evolution.The phylogenetic analysis based on whole chloroplast genome suggested that Acer species had divided into three significantly diverged clades into 10 already identified sections Platanoidea and Macrantha where these two were observed having a close relationship while A.yangbiense the previously newly discovered endemic maple as endangered species of China and formed its own smallest clade as a distinguishing factor in this study.Besides,our fossil-calibrated based molecular phylogenies date the crown of the genus Acer to Eocene with information for fast diversification events during few geological periods,and divergence occurred 34.9 million years ago(Mya)(95% HPD,22.8-49.7 Mya).Acer and its sister genus Dipteronia showed their occurrences in the Tertiary of North America and Asia and both are well represented in the fossil record.These whole chloroplast genome-based results provide useful genetic information for studying taxonomy,phylogeny,and species evolution of Aceraceae.